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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ) $local_species = 'hma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ) $local_species = 'lsa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ) $local_species = 'shi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ) $local_species = 'spa' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ), 'gf_id' => 'HOM05D001294', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001294' ), 'data_identifier' => 'HOM05D001294', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001294', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '485', 'num_species' => '99' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A02p04960' => 'bna', 'A03p00850' => 'bna', 'A03p08910' => 'bna', 'A05p39480' => 'bna', 'A07p30750' => 'bna', 'A07p34690' => 'bna', 'A10p21040' => 'bna', 'Aa31LG11G11090' => 'aar', 'Aa31LG2G1730' => 'aar', 'Aa31LG3G2020' => 'aar', 'Aa31LG9G90' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_117.691' => 'aag', 'Actinidia11239' => 'ach', 'Actinidia19736' => 'ach', 'Actinidia28277' => 'ach', 'Ah.01g007670' => 'amhyb', 'Ah.01g007680' => 'amhyb', 'Ah.07g204840' => 'amhyb', 'Ah.08g212340' => 'amhyb', 'Ah.08g212350' => 'amhyb', 'Ah.12g053270' => 'amhyb', 'AL3G20740' => 'aly', 'AL6G11920' => 'aly', 'AL6G29790' => 'aly', 'AL7G47050' => 'aly', 'AL7G50890' => 'aly', 'Aqoxy1G01360' => 'aox', 'Aqoxy1G01364' => 'aox', 'Aqoxy1G01419' => 'aox', 'Aqoxy1G01422' => 'aox', 'Aqoxy1G01554' => 'aox', 'Aqoxy2G00668' => 'aox', 'Aqoxy3G01089' => 'aox', 'Aqoxy4G00516' => 'aox', 'Aqoxy4G00520' => 'aox', 'Aqoxy4G02057' => 'aox', 'Aqoxy4G02088' => 'aox', 'Aqoxy4G02137' => 'aox', 'Aqoxy4G03081' => 'aox', 'Aqoxy4G03085' => 'aox', 'Aqoxy5G00119' => 'aox', 'Aqoxy5G04331' => 'aox', 'Aqoxy5G04382' => 'aox', 'arahy.Tifrunner.gnm1.ann1.6C98HC' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.FPLS03' => 'arhy', 'AT3G09570' => 'ath', 'AT5G02630' => 'ath', 'AT5G18520' => 'ath', 'AT5G42090' => 'ath', 'ATR0568G067' => 'atr', 'ATR0568G184' => 'atr', 'ATR0579G159' => 'atr', 'ATR0665G398' => 'atr', 'ATR0752G087' => 'atr', 'ATR0787G129' => 'atr', 'Atru.chr2.1112' => 'acertr', 'Atru.chr8.2499' => 'acertr', 'Atru.chr9.1851' => 'acertr', 'AUR62006019' => 'cqu', 'AUR62007065' => 'cqu', 'AUR62019930' => 'cqu', 'AUR62035607' => 'cqu', 'AUR62041002' => 'cqu', 'AUR62042137' => 'cqu', 'BcaB01g04902' => 'bca', 'BcaB01g06180' => 'bca', 'BcaB01g06183' => 'bca', 'BcaB01g06184' => 'bca', 'BcaB01g06195' => 'bca', 'BcaB01g06196' => 'bca', 'BcaB03g15106' => 'bca', 'BcaB03g15603' => 'bca', 'BcaB05g23334' => 'bca', 'BcaB08g36666' => 'bca', 'BcaB08g36670' => 'bca', 'BcaC02g08222' => 'bca', 'BcaC03g13605' => 'bca', 'BcaC04g18672' => 'bca', 'BcaC05g29685' => 'bca', 'BcaC08g45781' => 'bca', 'BcaC08g46257' => 'bca', 'BcaC08g46258' => 'bca', 'BolC2t06901H' => 'bol', 'BolC3t12670H' => 'bol', 'BolC3t13519H' => 'bol', 'BolC5t34501H' => 'bol', 'BolC6t38686H' => 'bol', 'BolC6t39254H' => 'bol', 'BolC9t58664H' => 'bol', 'BraA02t05455Z' => 'bra', 'BraA03t09468Z' => 'bra', 'BraA03t10217Z' => 'bra', 'BraA05t22729Z' => 'bra', 'BraA07t30713Z' => 'bra', 'BraA07t31087Z' => 'bra', 'BraA10t44168Z' => 'bra', 'C02p09940' => 'bna', 'C03p01100' => 'bna', 'C03p01110' => 'bna', 'C03p10390' => 'bna', 'C05p58500' => 'bna', 'C06p35640' => 'bna', 'C06p41730' => 'bna', 'C09p57970' => 'bna', 'CAN.G1117.4' => 'can', 'CAN.G1930.1' => 'can', 'CAN.G303.6' => 'can', 'CAN.G350.18' => 'can', 'CAN.G792.20' => 'can', 'CAN.G94.5' => 'can', 'CANSAT21G0164' => 'cansat', 'CANSAT80G1388' => 'cansat', 'CARHR083980' => 'chi', 'CARHR194500' => 'chi', 'CARHR210720' => 'chi', 'CARHR212440' => 'chi', 'Carub.0003s0866' => 'cru', 'Carub.0006s0145' => 'cru', 'Carub.0006s1679' => 'cru', 'Carub.0007s3324' => 'cru', 'Ca_08802_v3' => 'car', 'Ca_09588_v3' => 'car', 'Ca_16295_v3' => 'car', 'CBR_g28069' => 'cbr', 'CBR_g49976' => 'cbr', 'Cc02_g00940' => 'ccan', 'Cc06_g03210' => 'ccan', 'Cc08_g16850' => 'ccan', 'CDE02G2428' => 'cde', 'CDE02G3362' => 'cde', 'CDE04G0174' => 'cde', 'CDE04G0447' => 'cde', 'CDE06G0048' => 'cde', 'CDE07G1575' => 'cde', 'CDE09G1364' => 'cde', 'CDE11G0098' => 'cde', 'Cfa011913' => 'cfa', 'Cfa017458' => 'cfa', 'Ciclev10011742m.g' => 'ccl', 'Ciclev10020208m.g' => 'ccl', 'Ciclev10024007m.g' => 'ccl', 'CiPaw.09G186300' => 'cil', 'CiPaw.11G111400' => 'cil', 'CiPaw.16G021500' => 'cil', 'ClCG04G008620' => 'cla', 'ClCG10G000770' => 'cla', 'COL.COLO4_07092' => 'col', 'COL.COLO4_10810' => 'col', 'COL.COLO4_15537' => 'col', 'Cpa.g.sc114.17' => 'cpa', 'Cpa.g.sc15.137' => 'cpa', 'Cre12.g523950' => 'cre', 'CsaV3_3G000820' => 'csa', 'CsaV3_4G024540' => 'csa', 'CSS0016730' => 'camsi', 'CSS0036322' => 'camsi', 'CSS0042284' => 'camsi', 'CSS0043961' => 'camsi', 'CSS0044694' => 'camsi', 'DCAR_010577' => 'dca', 'DCAR_014560' => 'dca', 'DCAR_014948' => 'dca', 'DCAR_020864' => 'dca', 'DCAR_026506' => 'dca', 'Dinv18746' => 'din', 'Dinv29222' => 'din', 'Dinv35669' => 'din', 'Dinv37226' => 'din', 'Duzib068G1411' => 'dzi', 'Duzib093G1927' => 'dzi', 'Duzib106G0828' => 'dzi', 'Duzib128G0805' => 'dzi', 'Duzib128G1124' => 'dzi', 'Duzib205G0976' => 'dzi', 'ECA233G1710' => 'eca', 'ECA233G5790' => 'eca', 'ECA238G1294' => 'eca', 'ECA240G3723' => 'eca', 'ECA248G0580' => 'eca', 'EL10Ac3g05198' => 'bvu', 'EL10Ac7g17280' => 'bvu', 'Eucgr.E01051' => 'egr', 'Eucgr.G02451' => 'egr', 'Eucgr.K02574' => 'egr', 'Eucgr.K03178' => 'egr', 'FAN02G3032' => 'fan', 'FAN04G2149' => 'fan', 'FAN05G0008' => 'fan', 'FAN08G1403' => 'fan', 'FAN09G3814' => 'fan', 'FAN13G2204' => 'fan', 'FAN14G3897' => 'fan', 'FAN18G2815' => 'fan', 'FvH4_5g10800' => 'fve', 'FvH4_6g14730' => 'fve', 'Glyma.02G088300' => 'gma', 'Glyma.03G175000' => 'gma', 'Glyma.10G046500' => 'gma', 'Glyma.10G046600' => 'gma', 'Glyma.13G001000' => 'gma', 'Glyma.13G134600' => 'gma', 'Glyma.19G175700' => 'gma', 'Gohir.A02G098800' => 'ghi', 'Gohir.A04G078000' => 'ghi', 'Gohir.A09G159900' => 'ghi', 'Gohir.A11G018400' => 'ghi', 'Gohir.A11G018500' => 'ghi', 'Gohir.A11G018550' => 'ghi', 'Gohir.A11G299700' => 'ghi', 'Gohir.A12G240700' => 'ghi', 'Gohir.D03G085100' => 'ghi', 'Gohir.D04G117200' => 'ghi', 'Gohir.D09G155500' => 'ghi', 'Gohir.D11G018200' => 'ghi', 'Gohir.D11G018233' => 'ghi', 'Gohir.D11G018266' => 'ghi', 'Gohir.D11G314600' => 'ghi', 'Gohir.D12G242000' => 'ghi', 'Gorai.003G077500' => 'gra', 'Gorai.006G176900' => 'gra', 'Gorai.007G019200' => 'gra', 'Gorai.007G019300' => 'gra', 'Gorai.007G019400' => 'gra', 'Gorai.007G345700' => 'gra', 'Gorai.008G259300' => 'gra', 'Gorai.009G422200' => 'gra', 'GSVIVG01019665001' => 'vvi', 'GSVIVG01025585001' => 'vvi', 'GSVIVG01026321001' => 'vvi', 'GSVIVG01032618001' => 'vvi', 'HanXRQChr02g0052961' => 'han', 'HanXRQChr02g0052981' => 'han', 'HanXRQChr02g0053001' => 'han', 'HanXRQChr02g0053011' => 'han', 'HanXRQChr02g0053021' => 'han', 'HanXRQChr03g0085251' => 'han', 'HanXRQChr07g0204201' => 'han', 'HanXRQChr08g0225731' => 'han', 'HanXRQChr13g0399121' => 'han', 'HanXRQChr13g0414351' => 'han', 'Haze_09185' => 'cav', 'Haze_20702' => 'cav', 'Hma1.2p1_0094F.1_g047250' => 'hma', 'Hma1.2p1_0111F.1_g053350' => 'hma', 'Hma1.2p1_0350F.1_g132540' => 'hma', 'Hma1.2p1_0350F.1_g132550' => 'hma', 'Hma1.2p1_0456F.1_g156730' => 'hma', 'HPP92_019088' => 'vpl', 'HPP92_019348' => 'vpl', 'HPP92_020947' => 'vpl', 'HPP92_022474' => 'vpl', 'Lalb_Chr06g0171121' => 'lal', 'Lalb_Chr14g0362631' => 'lal', 'Lalb_Chr20g0113071' => 'lal', 'Lj1g0007808' => 'lja', 'Lj2C103T7' => 'lonja', 'Lj2C46T5' => 'lonja', 'Lj2P156T21' => 'lonja', 'Lj3A975T66' => 'lonja', 'Lj3P1059T42' => 'lonja', 'Lj3P897T71' => 'lonja', 'Lj5g0014018' => 'lja', 'Lj6g0013776' => 'lja', 'Lsat_1_v5_gn_1_54801' => 'lsa', 'Lsat_1_v5_gn_2_111400' => 'lsa', 'Lsat_1_v5_gn_3_114621' => 'lsa', 'Lsat_1_v5_gn_3_40920' => 'lsa', 'Lsat_1_v5_gn_3_40940' => 'lsa', 'Lsat_1_v5_gn_3_40980' => 'lsa', 'Lsat_1_v5_gn_4_115261' => 'lsa', 'Lsat_1_v5_gn_4_160520' => 'lsa', 'Lsat_1_v5_gn_4_161160' => 'lsa', 'Lsat_1_v5_gn_4_161360' => 'lsa', 'Lsat_1_v5_gn_4_161380' => 'lsa', 'Lsat_1_v5_gn_4_161420' => 'lsa', 'Lsat_1_v5_gn_4_161440' => 'lsa', 'Lsat_1_v5_gn_4_161480' => 'lsa', 'Lsat_1_v5_gn_4_181700' => 'lsa', 'Lsat_1_v5_gn_4_26840' => 'lsa', 'Lsat_1_v5_gn_4_26920' => 'lsa', 'Lsat_1_v5_gn_4_44741' => 'lsa', 'Lsat_1_v5_gn_4_50700' => 'lsa', 'Lsat_1_v5_gn_4_53341' => 'lsa', 'Lsat_1_v5_gn_4_53361' => 'lsa', 'Lsat_1_v5_gn_4_55901' => 'lsa', 'Lsat_1_v5_gn_4_63941' => 'lsa', 'Lsat_1_v5_gn_4_8141' => 'lsa', 'Lsat_1_v5_gn_4_9460' => 'lsa', 'Lsat_1_v5_gn_4_9541' => 'lsa', 'Lsat_1_v5_gn_6_33040' => 'lsa', 'Lsat_1_v5_gn_6_81701' => 'lsa', 'Lsat_1_v5_gn_7_15560' => 'lsa', 'Lsat_1_v5_gn_8_4561' => 'lsa', 'Manes.02G001900' => 'mes', 'Manes.09G088000' => 'mes', 'Manes.09G146700' => 'mes', 'Mapoly0114s0018' => 'mpo', 'MBI10_g16792_MAGBIO' => 'mbi', 'MBI12_g42136_MAGBIO' => 'mbi', 'MBI12_g44944_MAGBIO' => 'mbi', 'MBI14_g16290_MAGBIO' => 'mbi', 'MCO10G396' => 'mco', 'MD04G1116700' => 'mdo', 'MD06G1120800' => 'mdo', 'MD12G1132400' => 'mdo', 'MD14G1137400' => 'mdo', 'Medtr1g061930' => 'mtr', 'Medtr1g067370' => 'mtr', 'Medtr3g080830' => 'mtr', 'Medtr7g100360' => 'mtr', 'MELO3C003086.2' => 'cme', 'MELO3C013769.2' => 'cme', 'Migut.E00734' => 'egut', 'Migut.E01652' => 'egut', 'Migut.J00388' => 'egut', 'Migut.O00809' => 'egut', 'MSTRG.13708' => 'ama', 'MSTRG.19115' => 'ama', 'MSTRG.5702' => 'ama', 'Nitab4.5_0000202g0320' => 'nta', 'Nitab4.5_0000319g0210' => 'nta', 'Nitab4.5_0000643g0120' => 'nta', 'Nitab4.5_0000673g0200' => 'nta', 'Nitab4.5_0000841g0030' => 'nta', 'Nitab4.5_0002774g0010' => 'nta', 'Nitab4.5_0004109g0010' => 'nta', 'Nitab4.5_0005544g0030' => 'nta', 'Nitab4.5_0006713g0040' => 'nta', 'Nitab4.5_0011775g0020' => 'nta', 'Nn1g03005' => 'nnu', 'Nn2g10541' => 'nnu', 'Nn2g12841' => 'nnu', 'Nn3g18848' => 'nnu', 'Oeu010734.1' => 'oeu', 'Oeu010735.1' => 'oeu', 'Oeu023877.2' => 'oeu', 'Oeu035169.1' => 'oeu', 'Oeu042838.1' => 'oeu', 'Oeu055380.1' => 'oeu', 'Oeu060065.1' => 'oeu', 'Os01g0836700' => 'osa', 'Os01g0836800' => 'osa', 'Os02g0618700' => 'osa', 'Os04g0508600' => 'osa', 'Os05g0462500' => 'osa', 'Os06g0132100' => 'osa', 'Peaxi162Scf00039g00429' => 'pax', 'Peaxi162Scf00077g00106' => 'pax', 'Peaxi162Scf00300g00083' => 'pax', 'Peaxi162Scf00542g00626' => 'pax', 'Peaxi162Scf00604g00005' => 'pax', 'Peaxi162Scf01257g00006' => 'pax', 'PGR004G1586' => 'pgr', 'PGR031G2505' => 'pgr', 'PGR142G0789' => 'pgr', 'PGSC0003DMG400003221' => 'stu', 'PGSC0003DMG400011055' => 'stu', 'PGSC0003DMG400023915' => 'stu', 'PGSC0003DMG400030229' => 'stu', 'PGSC0003DMG401005859' => 'stu', 'Phvul.001G172000' => 'pvu', 'Phvul.006G008660' => 'pvu', 'Phvul.007G160700' => 'pvu', 'Potri.001G083100' => 'ptr', 'Potri.003G147700' => 'ptr', 'Potri.006G214900' => 'ptr', 'Potri.013G049500' => 'ptr', 'Potri.016G081300' => 'ptr', 'Pp3c10_16540' => 'ppa', 'Pp3c14_13380' => 'ppa', 'PRCOL_00004716' => 'pco', 'Prupe.5G131400' => 'ppe', 'Prupe.6G246500' => 'ppe', 'Psat3g048040' => 'psa', 'Psat5g110160' => 'psa', 'Psat6g069480' => 'psa', 'PSO063G7159' => 'pso', 'PSO206G0050' => 'pso', 'PSO339G4401' => 'pso', 'PSO384G3408' => 'pso', 'PSO699G0008' => 'pso', 'PSO782G4998' => 'pso', 'QL02p027727' => 'qlo', 'QL07p046074' => 'qlo', 'QL11p011980' => 'qlo', 'QL11p044024' => 'qlo', 'QL12p039454' => 'qlo', 'RcHm_v2.0_Chr3g0467951' => 'rch', 'RcHm_v2.0_Chr7g0187361' => 'rch', 'Rhsim02G0252900' => 'rsi', 'Rhsim05G0008200' => 'rsi', 'Rhsim05G0008400' => 'rsi', 'Rhsim05G0015900' => 'rsi', 'Rhsim05G0021500' => 'rsi', 'Rhsim07G0181900' => 'rsi', 'Rhsim09G0209100' => 'rsi', 'Sabra01G0059700' => 'sbr', 'Sabra03G0107400' => 'sbr', 'Sabra06G0165900' => 'sbr', 'Sabra13G0045700' => 'sbr', 'Sabra16G0089300' => 'sbr', 'Sabra16G0090600' => 'sbr', 'SalBow3G4336' => 'sbo', 'SalBow8G4939' => 'sbo', 'Sc01g0003820' => 'sci', 'Sc01g0010770' => 'sci', 'Sc09g0001830' => 'sci', 'Sc09g0001840' => 'sci', 'Sc13g0010180' => 'sci', 'Sed0011258' => 'sed', 'Sed0013144' => 'sed', 'Sed0027112' => 'sed', 'SEGI_08840' => 'sgi', 'SEGI_18799' => 'sgi', 'SEGI_19129' => 'sgi', 'SEGI_24316' => 'sgi', 'SEGI_35404' => 'sgi', 'SGA_v2.0_scaffold126G33858' => 'sas', 'SGA_v2.0_scaffold267G46177' => 'sas', 'SGA_v2.0_scaffold63G21738' => 'sas', 'SGA_v2.0_scaffold75G24907' => 'sas', 'SHI12651' => 'shi', 'SMO147G0305' => 'smo', 'SMO348G0018' => 'smo', 'Solyc03g082440.1' => 'sly', 'Solyc04g050260.1' => 'sly', 'Solyc08g008650.1' => 'sly', 'Solyc09g005920.4' => 'sly', 'Solyc10g084530.1' => 'sly', 'Sopen03g022160' => 'spe', 'Sopen08g004480' => 'spe', 'Sopen09g001780' => 'spe', 'Sopen10g033950' => 'spe', 'Sp3g07920' => 'spa', 'Sp6g25810' => 'spa', 'Sp7g00040' => 'spa', 'TAR362G0820' => 'tar', 'TAR369G0602' => 'tar', 'TAR629G0779' => 'tar', 'TAR633G0681' => 'tar', 'TAR636G2270' => 'tar', 'TAR636G2891' => 'tar', 'THA.LOC104805384' => 'tha', 'THA.LOC104806510' => 'tha', 'THA.LOC104809297' => 'tha', 'THA.LOC104827000' => 'tha', 'Thecc.03G219600' => 'tca', 'Thecc.05G048200' => 'tca', 'Thecc.05G266600' => 'tca', 'Thhalv10013548m.g' => 'esa', 'Thhalv10028347m.g' => 'esa', 'TPR.G10538' => 'tpr', 'TPR.G21322' => 'tpr', 'TPR.G30400' => 'tpr', 'TPR.G36236' => 'tpr', 'TPR.G40294' => 'tpr', 'TPR.G40297' => 'tpr', 'TWI15G0755' => 'twi', 'TWI53G1505' => 'twi', 'TWI60G0829' => 'twi', 'TWI74G1677' => 'twi', 'unitig_22.g5079' => 'ugi', 'unitig_22.g5637' => 'ugi', 'unitig_27.g25272' => 'ugi', 'unitig_578.g15711' => 'ugi', 'unitig_8.g3577' => 'ugi', 'vmacro08677' => 'vma', 'vmacro10153' => 'vma', 'vmacro17142' => 'vma', 'vmacro17208' => 'vma', 'vmacro17209' => 'vma', 'VMungo0251G2400' => 'vmu', 'VMungo0720G0331' => 'vmu', 'VMungo1383G2281' => 'vmu', 'VMungo1383G2707' => 'vmu', 'Zm00001eb077820' => 'zma', 'Zm00001eb148690' => 'zma', 'Zm00001eb247380' => 'zma', 'Zm00001eb269770' => 'zma', 'Zm00001eb289810' => 'zma', 'Zm00001eb351490' => 'zma', 'Zm00001eb368150' => 'zma', 'Zm00001eb378170' => 'zma', 'Zm00001eb378180' => 'zma', 'Zm00001eb426290' => 'zma' ) $gf_id = 'HOM05D001294' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001294' ) $data_identifier = 'HOM05D001294' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 15, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 6, 'aly' => (int) 5, 'aox' => (int) 17, 'arhy' => (int) 2, 'ath' => (int) 4, 'atr' => (int) 6, 'acertr' => (int) 3, 'cqu' => (int) 6, 'bca' => (int) 18, 'bol' => (int) 7, 'bra' => (int) 7, 'can' => (int) 6, 'cansat' => (int) 2, 'chi' => (int) 4, 'cru' => (int) 4, 'car' => (int) 3, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 8, 'cfa' => (int) 2, 'ccl' => (int) 3, 'cil' => (int) 3, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 4, 'dzi' => (int) 6, 'eca' => (int) 5, 'bvu' => (int) 2, 'egr' => (int) 4, 'fan' => (int) 8, 'fve' => (int) 2, 'gma' => (int) 7, 'ghi' => (int) 16, 'gra' => (int) 8, 'vvi' => (int) 4, 'han' => (int) 10, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 4, 'lal' => (int) 3, 'lja' => (int) 3, 'lonja' => (int) 6, 'lsa' => (int) 30, 'mes' => (int) 3, 'mpo' => (int) 1, 'mbi' => (int) 4, 'mco' => (int) 1, 'mdo' => (int) 4, 'mtr' => (int) 4, 'cme' => (int) 2, 'egut' => (int) 4, 'ama' => (int) 3, 'nta' => (int) 10, 'nnu' => (int) 4, 'oeu' => (int) 7, 'osa' => (int) 6, 'pax' => (int) 6, 'pgr' => (int) 3, 'stu' => (int) 5, 'pvu' => (int) 3, 'ptr' => (int) 5, 'ppa' => (int) 2, 'pco' => (int) 1, 'ppe' => (int) 2, 'psa' => (int) 3, 'pso' => (int) 6, 'qlo' => (int) 5, 'rch' => (int) 2, 'rsi' => (int) 7, 'sbr' => (int) 6, 'sbo' => (int) 2, 'sci' => (int) 5, 'sed' => (int) 3, 'sgi' => (int) 5, 'sas' => (int) 4, 'shi' => (int) 1, 'smo' => (int) 2, 'sly' => (int) 5, 'spe' => (int) 4, 'spa' => (int) 3, 'tar' => (int) 6, 'tha' => (int) 4, 'tca' => (int) 3, 'esa' => (int) 2, 'tpr' => (int) 6, 'twi' => (int) 4, 'ugi' => (int) 5, 'vma' => (int) 5, 'vmu' => (int) 4, 'zma' => (int) 10 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb426290' $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